In the chicken genome there are large regions occupied not by structural genes but by repetitive DNA sequences in which many of the cytosine residues have been methylated to 5-methyl cytosine. We are determining the detailed structure and function of these methylated repetitive regions. We study their organization by molecular cloning, by Southern transfer hybridization experiments, and by in situ hybridization to metaphase chromosomes. We have determined their pattern of methylation in sperm, embryonic stages, adult tissues, contemporary populations, and in avian species related to chickens. Methylation is maintained in all DNA samples mentioned above. By direct DNA sequencing we have analyzed the nucleotide sequences that surround these methylated bases. These DNA sequences have also been used in analysis of DNA binding proteins isolated from nuclei. Completion of this work will provide a full description of the structure of some persistently methylated repeated DNA sequences and the influence of methylation on DNA-protein interactions.